As of 2014, Koonin serves on the advisory editorial board of Trends in Genetics, and is co-Editor-in-Chief of the open access journal Biology Direct. He served on the editorial board of Bioinformatics from 1999-2001. Koonin is also an advisory board member in bioinformatics at Faculty of 1000.
Koonin, the logic of chance, page 214:
Arguments for a LUCA that would be indistinguishable from a modern prokaryotic cell have been presented, along with scenarios depicting LUCA as a much more primitive entity (Glansdorff, et al., 2008).
The difficulty of the problem cannot be overestimated. Indeed, all known cells are complex and elaborately organized. The simplest known cellular life forms, the bacterial (and the only known archaeal) parasites and symbionts, clearly evolved by degradation of more complex organisms; however, even these possess several hundred genes that encode the components of a fully fledged membrane; the replication, transcription, and translation machineries; a complex cell-division apparatus; and at least some central metabolic pathways. As we have already discussed, the simplest free-living cells are considerably more complex than this, with at least 1,300 genes.
All the difficulties and uncertainties of evolutionary reconstructions notwithstanding, parsimony analysis combined with less formal efforts on the reconstruction of the deep past of particular functional systems leaves no serious doubts that LUCA already possessed at least several hundred genes. In addition to the aforementioned “golden 100” genes involved in expression, this diverse gene complement consists of numerous metabolic enzymes, including pathways of the central energy metabolism and the biosynthesis of amino acids, nucleotides, and some coenzymes, as well as some crucial membrane proteins, such as the subunits of the signal recognition particle (SRP) and the H+- ATPase.
The reconstructed gene repertoire of LUCA also has gaping holes. The two most shocking ones are (i) the absence of the key components of the DNA replication machinery, namely the polymerases that are responsible for the initiation (primases) and elongation of DNA replication and for gap-filling after primer removal, and the principal DNA helicases (Leipe, et al., 1999), and (ii) the absence of most enzymes of lipid biosynthesis. These essential proteins fail to make it into the reconstructed gene repertoire of LUCA because the respective processes in bacteria, on one hand, and archaea, on the other hand, are catalyzed by different, unrelated enzymes and, in the case of membrane phospholipids, yield chemically distinct membranes.
Schocking and remarkable indeed :
The DNA replication machinery is essential in all domains, and so is lipid biosynthesis for cell membranes. Its not possible that the first cells emerged without membranes and DNA replication in a LUCA, and then evolved distinguished membranes and DNA replication, each by its own.
That means, the at least several hundred genes possessed in all tree domains of life would have had to emerge in a convergent manner ( that is separately they would have come into existence with the same genome, proteome and metabolome except lipid biosynthesis and DNA replication which were the two only distinct parts that diverged each from the other domains. This is a hard sell when evoking evolution. Even more when only unguided random mechanisms were at hand, that is chance and luck. If the emergency of one cell type would have been exceedingly improbable, imagine the same feat tree separate times. As Stephen J. Gould wrote in Wonderful Life: The Burgess Shale and the Nature of History :
“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1
Neither a LUCA is credible, nor naturally emerging tree separate domains of life through partially convergent manner. The only rational explanation is a designer creating the tree domains of life separately, and using the same toolkit where required, and a separate divergent toolkit for other parts.
Should that not be evidence that a LUCA never existed, and that the three domains of life had to emerge separately through a intelligent designer ?
The widespread role of non-enzymatic reactions in cellular metabolism
Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes 14
Evolution of the coordinate regulation of glycolytic enzyme genes by hypoxia
There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides 15
Genetic, protein and DNA analysis, together with major differences in the biochemistry and molecular biology of between all three domains – Bacteria, Archaea and Eukaryota – suggest that the three fundamental cell types are distinct and evolved separately (i.e. Bacteria are not actually pro-precursors of the eukaryotes, which have sequence similarities in particular parts of their biochemistry between both Bacteria or Archaea). Only a relatively small percentage of genes in Archaea have sequence similarity to genes in Bacteria or Eukaryota. Furthermore, most of the cellular events triggered by intracellular Ca2+ in eukaryotes do not occur in either Bacteria or Archaea.
Prokaryotic evolution and the tree of life are two different things
The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.
The network of life: genome beginnings and evolution
The rapid growth of genome-sequence data since the mid-1990s is now providing unprecedented detail on the genetic basis of life, and not surprisingly is catalysing the most fundamental re-evaluation of origins and evolution since Darwin’s day. Several papers in this theme issue argue that Darwin’s tree of life is now best seen as an approximation—one quite adequate as a description of some parts of the living world (e.g. morphologically complex eukaryotes), but less helpful elsewhere (e.g. viruses and many prokaryotes); indeed, one of our authors goes farther, proclaiming the “demise” of Darwin’s tree as a hypothesis on the diversity and seeming naturalness of hierarchical arrangements of groups of living organisms.
Uprooting the Tree of Life
Charles Darwin contended more than a century ago that all modern species diverged from a more limited set of ancestral groups, which themselves evolved from still fewer progenitors and so on back to the beginning of life. In principle, then, the relationships among all living and extinct organisms could be represented as a single genealogical tree.Most contemporary researchers agree. Many would even argue that the general features of this tree are already known, all the way down to the root—a solitary cell, termed life’s last universal common ancestor, that lived roughly 3.5 to 3.8 billion years ago. The consensus view did not come easily but has been widely accepted for more than a decade. Yet ill winds are blowing. To everyone’s surprise, discoveries made in the past few years have begun to cast serious doubt on some aspects of the tree, especially on the depiction of the relationships near the root.
marine worms are more closely related to humans than are mollusks and insects - Nature 2-9-11
Newly Discovered 'Orphan Genes' Defy Evolution 2
An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.
Many multicellular animals share similar sets of genes that produce proteins that perform related biochemical functions. This is a common feature of purposefully engineered systems. In addition to these standard genes, all organisms thus far tested also have unique sets of genes specific to that type of creature.
The authors of a recent review paper, published in Trends in Genetics, on the subject of orphan genes stated, "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species."1
These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature's interaction with its environment.2 The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms). And several new studies in both fish and insect genomes are now highlighting this important fact.
What Is the Tree of Life?
A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic. 12 One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” . Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain [2–4].
Octopuses ‘are aliens’, scientists decide after DNA study
Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.
The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.
There we were thinking it was quite freaky enough when they learned how to open jam jars.
US researcher Dr Clifton Ragsdale, from the University of Chicago, said: ;The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain and its clever problem-solving abilities.
‘The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our paper describes the first sequenced genome from an alien.’
Octopuses: What even ARE they?
They inhabit every ocean at almost all depths and possess a range of features that call to mind sci-fi aliens.
These include prehensile sucker-lined tentacles, highly mobile, camera-like eyes sensitive to polarised light, sophisticated camouflage systems that alter skin colour and patterns, jet-propulsion, three hearts, and the ability to regenerate severed limbs.
The scientists estimate that the two-spot octopus genome contains 2.7 billion base pairs – the chemical units of DNA – with long stretches of repeated sequences.
Octopus Have Been Found to have Unique Genes
hundreds of other genes that are common in cephalopods, but unknown in other animals, were found.
Decoding the genome of an alien
Besides recognizable genes, vast swathes of the genome consist of regulatory networks that control how genes are expressed in cells. In the octopus, nearly half of the genome was found to be composed of mobile elements called transposons, one of the highest proportions in the animal kingdom. Transposons replicate and move around with a life of their own, disrupting or enhancing gene expression and facilitating reshufflings of gene order. The researchers found many of them to be particularly active in the octopus nervous system. The "Hox" genes, involved in embryonic development in all animals, are a particularly dramatic example. Although clustered together in most animals, including other mollusks, they are scattered in snippets in the octopus, presumably enabling the evolution of the versatile cephalopod body plan.
Presumably. Yes. Or , in other words, guess work as always...... The architecture of a body plan must be right from the beginning. Everything goes, or nothing goes. The question is, where does the information of this reshuffling of genes came from ? In my view, the only rational explanation is intentional design.
Are Rotifers Gene Stealers or Uniquely Engineered? 1
The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer.1
In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA. They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.
Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent. Further complicating this picture, the rotifer gene sequences were found in a diverse number of non-rotifer creatures! Some of the creatures that had gene matches to rotifers included a variety of plants, other multicellular animals, protists (complex single celled animals), archaea, bacteria, and fungi. Evolutionists have two options in which to categorize these unusual gene matches based on their naturalistic presuppositions. First, they can say that these genes evolved independently in separate creatures in a hypothetical process called "convergent evolution." However, in cases where there are literally hundreds of these DNA sequences popping up in multiple organisms, this scenario becomes so unlikely that even evolutionists have too much difficulty imagining it. The second option is called "horizontal gene transfer," or HGT. This involves the transfer of genes, perhaps via some sort of microbial host vector such as a bacterium.2
What a bust against common ancestry from a mainstream scientist :
The Biological Big Bang model for the major transitions in evolution
Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.
The argument of the broken down evolution tree
1. The fundamental tenet of evolution theory is that species evolved according to the evolutionary tree; one after the other evolved, as a genealogical family tree.
2. However, since Darwin, science has continued to document exceptions and anomalies—species that don’t fit neatly into the evolutionary pattern.
-- For example, species that in many regards appear to be quite similar, which evolutionists have placed on neighboring twigs of the evolutionary tree, are routinely found to have profound differences. Here is an example:
a. In 2010 an article in the journal Nature released the results of a human-chimp DNA study with implications that was very surprising for the scientific community because the result of the research contradicted the long-held hypothesis of their similarity.
b. Already the title summed up the research findings: "Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content."
c. The chimpanzee DNA sequence for a chromosome was assembled and oriented based on a Y chromosome map/framework built for chimpanzee and not human. As a result, the chimpanzee DNA sequence could then be more accurately compared to the human Y chromosome.
d. The chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome.
c. The researchers also sought to determine if there was any difference in actual gene categories and they found a shocking 33 percent difference.
e. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps.
f. Because virtually every structural aspect of the human and chimp Y chromosomes was different, it was hard to arrive at an overall similarity estimate between the two. The researchers did postulate an overall 70 percent similarity, which did not take into account size differences or structural arrangement differences. This was done by concluding that only 70 percent of the chimp sequence could be aligned with the human sequence--not taking into account differences within the alignments. I.O.W. 70 percent was a conservative estimate, especially when considering that 50 percent of the human genes were missing from the chimp, and that the regions that did have some similarity were located in completely different patterns. When all aspects of non-similarity--sequence categories, genes, gene families, and gene position--are taken into account, it is safe to say that the overall similarity was lower than 70 percent.
g. The Nature article we can read, "Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation."
h. So, the human Y chromosome looks just as different from a chimp as the other human chromosomes do from a chicken. And to explain where all these differences between humans and chimps came from, believers in big-picture evolution are forced to invent stories of major chromosomal rearrangements and rapid generation of vast amounts of many new genes, along with accompanying regulatory DNA.
i. However, since each respective Y chromosome appears fully integrated and interdependently stable with its host organism, the most logical inference from the Y chromosome data is that humans and chimpanzees were each specially created as distinct creatures.
-- On the other hand, species that are obviously quite different, which evolutionists have placed on distant limbs of the evolutionary tree, are often found to have profound similarities.
a. Humans, Arabidopsis (A genus of the mustard-family having white, yellow or purplish flowers), and nematodes (Unsegmented worms with elongated rounded body pointed at both ends) all have about the same number of genes.
a. A research team from Heidelberg from the European Molecular Biology Laboratory [EMBL], compared human and fruit-fly introns with those of a roundworm thought to be 600 million years old. Surprisingly, introns were already in the worms from the beginning of their appearance and remained the same all the way to the human line, changing rapidly and losing many of them only in other species like insects. One of the researchers remarked, “Now we have direct evidence that genes were already quite complex in the first animals, and many invertebrates have reduced part of this complexity.” Yet another said, “The worm’s genes are very similar to human genes…That’s a much different picture than we’ve seen from the quickly-evolving species that have been studied so far.” Additionally, the genome too “has been preserved over the last half a billion years.” In their research they did not explain how the early-Cambrian roundworms got their complexity and ability to remain unchanged for millions of years. The discovery is obviously changing the evolution tree.
b. Molecular evolution trees often do not fit a morphology-based evolution tree. For example, there are several TRAF genes in humans and Drosophila, and obvious prediction of Darwin’s model is that there must be an ancestral gene in a common ancestral organism from which the modern TRAF genes were derived. In reality, however, a TRAF gene from Hydra does not fit criteria of an ancestral gene, which must be somewhat of a mix of all human TRAF families, but rather clearly belongs to the major group of TRAF genes along with human TRAF1, TRAF2, TRAF3 and TRAF 5, while human TRAF4 and especially TRAF6 belong to different groups together with Drosophila TRAFs. 
3. For years evolutionists attempted to explain the growing list of contradictions using their evolutionary tree model. But it is obvious that this was an exercise in forcing the evidence to fit the theory rather than the other way around.
4. In recent years evolutionists have finally begun to deemphasize their iconic evolutionary tree model. What this does not change, however, is their insistence that evolution is a fact.
5. Thus, even nowadays students are taught that the species fall into the expected tree pattern. But some venturesome writers are beginning to mention this unmentionable, foridden archeology.
6. Few years ago, for instance, the Telegraph reported that “Charles Darwin's tree of life is ‘wrong and misleading.’
-- They believe the concept misleads us because his [Darwin’s] theory limits and even obscures the study of organisms and their ancestries. …
-- Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded. …
-- “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.” …
-- More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either. …
-- Dr Rose said: "The tree of life is being politely buried – we all know that. What's less accepted is our whole fundamental view of biology needs to change." He says biology is vastly more complex than we thought and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.
7. Contrary evidences were/are continuously openly discussed. But none of them is allowed to cast any doubt on evolutionary theory itself. As the article reported:
8. "If you don't have a tree of life what does it mean for evolutionary biology? At first it's very scary – but in the past couple of years people have begun to free their minds." Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe.
9. The theory has to be repeatedly modified and augmented to try to fit the data. At some point the theory becomes little more than a tautology. Namely, whatever discovery is made in biology, evolution must have created it, no matter how contradictory and unlikely.
10. However such tautology is one of the fallacies in logic. By definition:
"Tautology in formal logic refers to a statement that must be true in every interpretation by its very construction. In rhetorical logic, it is an argument that utilizes circular reasoning, which means that the conclusion is also its own premise. Typically the premise is simply restated in the conclusion, without adding additional information or clarification. The structure of such arguments is A=B therefore A=B, although the premise and conclusion might be formulated differently so it is not immediately apparent as such."
11. Thus the only logical explanation of differences between similar species and similarities of different species is an involvement of an intelligent designer using similar genetic patterns. This all men call God.
12. God exists.
1. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii F. Raible, K. Tessmar-Raible, K. Osoegawa, P. Wincker, C. Jubin, G. Balavoine, D. Ferrier, V. Benes, P. de Jong, J. Weissenbach, P. Bork and D. Arendt.
2. intron - Part of a gene whose sequence is transcribed but not present in a mature mRNA after splicing.
3. Mali B, Frank U. Hydroid TNF-receptor-associated factor (TRAF) and its splice variant: a role in development.Mol Immunol. (2004) 41:377-84
4. Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.
At about the same time, Dalhousie University evolutionary biologist W. Ford Doolittle concluded that lateral gene transfer among ancient organisms meant that molecular phylogeny might never be able to discover the “true tree” of life, not because it is using the wrong methods or the wrong genes, “but because the history of life cannot properly be represented as a tree.” He concluded: “Perhaps it would be easier, and in the long run more productive, to abandon the attempt to force” the molecular data “into the mold provided by Darwin.” Instead of a tree, Doolittle proposed “a web- or net-like pattern.” 10
The controversy over the universal tree of life continues. In 2002, Woese suggested that biology should go beyond Darwin’s doctrine of common descent. In 2004, he wrote: “The root of the universal tree is an artifact resulting from forcing the evolutionary course into a tree representation when that representation is inappropriate.” In 2004, Doolittle and his colleagues proposed replacing the tree of life with a net-like “synthesis of life,” and in 2005 they recommended that “representations other than a tree should be investigated.” Meanwhile, other scientists continue to defend the hypothesis that the universal ancestor existed but was complex rather than simple 11
“DR ROSE SAID: ‘THE TREE OF LIFE IS BEING POLITELY BURIED – WE ALL KNOW THAT. WHAT’S LESS ACCEPTED IS OUR WHOLE FUNDAMENTAL VIEW OF BIOLOGY NEEDS
TO CHANGE.’ HE SAYS BIOLOGY IS VASTLY MORE COMPLEX THAN WE THOUGHT AND FACING UP TO THIS COMPLEXITY WILL BE AS SCARY AS THE CONCEPTUAL UPHEAVALS PHYSICISTS HAD TO TAKE ON BOARD IN THE EARLY 20TH CENTURY.”
The Rooting of the Universal Tree of Life Is Not Reliable 5
Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.
Early evolution without a tree of life 6
There is more to evolution than will fit on any tree. For understanding major transitions in early evolution, we might not need a tree of life at all. But we need to keep our ideas testable with data from genomes or other independent data so as to keep our nose pinned to the grindstone of observations. The very early evolution of life is mostly written in the language of chemistry, some of which is (arguably) still operating today in modern metabolism if we look at the right groups . The environments and starting material that the Earth had to offer to fuel early chemistry are variables that only geochemists can reasonably constrain . One can make a case that acetogens (clostridial firmicutes) and hydrogenotrophic methanogens (euryarchareotes) harbour the ancestral states of microbial physiology in the eubacteria and archaebacteria respectively , and some trees are compatible with that view , as is the distribution of primitive energy-conserving mechanisms . But given a transition from the elements on early Earth to replicating cells, the course of prokaryote evolution does not appear to play out along the branches of a phylogenetic tree. For example, Whitman surveyed the biology and diversity of prokaryotes, showing an rRNA tree to discuss matters of classification; but branching orders in that tree play no role in his discussion of diversity or underlying evolutionary processes. If that is the direction we are headed , it is not all bad. But having the eukaryotes sitting on one branch in the rRNA tree of life rather than on two, as they should be (or three in the case of plants with their plastids), is far enough off the mark that we should be striving for a better representation of the relationship of eukaryotes to the two kinds of prokaryotes from which they stem.
Eukaryotes are genetic chimaeras and the role of mitochondria in the origin of that chimaerism is apparent . Eukaryotes are complex and the pivotal role of mitochondria in the origin of that complexity (as opposed to a pivotal role of phagocytosis) seems increasingly difficult to dispute, for energetic reasons . That leaves little reasonable alternative to the view that the host for the origin of mitochondria was a prokaryote, in the simplest of competing alternatives an archaebacterium . The antiquity of anaerobic energy metabolism and sulfide metabolism among eukaryotes meshes well with newer views of Proterozoic ocean chemistry . A challenge remains in computing networks of genomes that include lateral gene transfers among prokaryotes and the origin of eukaryotes in the same graph. Tracking early evolution without a tree of life affords far more freedom to explore ideas than thinking with a tree in hand. The ideas need to generate predictions and be testable, though, otherwise they are not science. If we check our thoughts too quickly against a tree whose truth nobody can determine anyway, the tree begins to decide which thoughts we may or may not have and which words we may or may not use. Should a tree of life police our thoughts? Working without one is an option.
Pattern pluralism and the Tree of Life hypothesis 7
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or fordifferent purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.
A Common Evolutionary Origin for Tailed-Bacteriophage Functional Modules and Bacterial Machineries 8
The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages. For instance, sequence similarity between Siphoviridae major tail proteins (MTPs), which have been experimentally demonstrated to form the phage tail tube, is often not detectable
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage 9
Phage do not contain a ribosomal sequence that allows them to be placed on the universal tree of life and, to date, have not benefited from their own gene-based taxonomic system. Previous attempts to classify and measure phage biodiversity based on genetic markers have met with limited success. Although structural proteins (e.g., capsids) could hypothetically serve as a basis for phage taxonomy (27, 29, 41, 60), they are highly diverse and, unlike rDNAs, do not contain conserved regions that allow them to be easily identified. This limits the usefulness of these proteins as markers for biodiversity studies. We show here that no single gene is found in all phage that can be used as the basis for a classification system.
What Exactly Does Genetic Similarity Demonstrate? 1
Origin of genes with unresolved ancestry
The Main Issue: Unintelligent vs. Intelligent Mechanism
My hope is that one day thinking about Darwinian Theory will become clearer in the public square. Recall that Darwin made two claims: (1) all living beings descend from one or a few original ancestors, and (2) the mechanism driving the changes among species is the blind, unguided mechanism of natural selection.
The controversial claim, of course, is the second one--the idea that a purely material mechanism, without any intelligence involved, is responsible for all of the genetic information necessary for life (DNA) and hence for all of life's diversity.
Sequence Similarity Alone Does NOT Prove Common Ancestry
the 98.8% DNA sequence similarity between chimps and humans that Clines references does not even establish claim one (common ancestry). And "you don't have to take my word for it," as LeVar Burton always used to say on Reading Rainbow.
As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities
"This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles.
We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity.
Some design proponents think the evidence for common ancestry is good (e.g., Michael Behe), while others--citing the fossil record, especially The Cambrian Explosion--do not. But neither group thinks that sequence similarity alone proves either common ancestry or the Darwinian mechanism, as so many science writers of our day seem eager to assume.
More than just orphans: are taxonomically-restricted genes important in evolution? 2
Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes.
Similarities between living organisms could be because they have been designed by the same intelligence, just as we can recognize a Norman Foster building by his characteristic style , or a painting by Van Gogh. 3 We expect to see repeated motifs and re-used techniques in different works by the same artist/designer.
In addition, similarities can be interpreted as evidence for design economy. Why should a designer come up with, for example, a new system of genetic code for each type of organism? Why should basic metabolic pathways or the universal energy currency differ between organisms? They do not need to because an intelligent designer can build diversity around common features.
Part of the reason for similarity in design, is that organisms have similar demands placed upon them, which can only be met in a limited number of ways. All cars have wheels, not because they have evolved from each other, but because the car designing community recognizes wheels as an efficient way of moving over a flat surface. In the same way there are limited ways of respiring, photosynthesizing or transporting energy.
If similarity is evidence for common ancestry, then does its opposite – dissimilarity – provide evidence against common ancestry?
There is, of course, much dissimilarity between living organisms, some of these at a very fundamental level. For example, the standard system of genetic code used by humans is not universal. Eighteen different genetic codes have been found in various species. Many scientists see this as evidence that all life does not come from a single common ancestor.
Similar genes and proteins in organisms are taken as evidence for common ancestry. But :
as we sequence more and more genomes, we repeatedly find genes which are unique to organisms. These are known as ORFans, and provide a real conundrum for evolutionists.
The DNA sequences of humans and chimpanzees are 96% similar, but the 4% difference represents 40 million individual differences at the nucleotide level.
When genes and proteins are used to try to reconstruct the ancestry of different organisms, and how they are linked in a tree-like pattern, different sources of evidence give different results. Different genes and proteins have conflicting patterns of similarity and difference between organisms. Evolutionists can only get round this problem by working out the most efficient way in which evolution could have worked. When they do this, they have to come up with scenarios where some similarities between organisms are not due to common ancestry, but to convergent evolution. This raises another problem: if similarities are not always due to common ancestry, how can they be evidence for common ancestry?
If the living world is designed, the patterns of similarity and difference we see in the living world could be due to selective use of designed modules to produce different combinations of features.
Comparative biochemistry and cell biology does not give clear evidence for macro-evolution. In fact, recent discoveries such as the non-universality of the genetic code are strong arguments against common ancestry. The patterns of similarity and difference in living organisms are fully consistent with design.
Common DNA Sequences: Evidence of Evolution or Efficient Design?
With the advent of modern biotechnology, researchers have been able to determine the actual sequence of the roughly three billion bases of DNA (A,T,C,G) that make up the human genome. They have sequenced the genomes of many other types of creatures as well. Scientists have tried to use this new DNA data to find similarities in the DNA sequences of creatures that are supposedly related through evolutionary descent, but do genetic similarities provide evidence for evolution?
DNA Supports Distinct Kinds
In the June 2009 Acts & Facts, an article was published by the author that showed how this approach has been used in an attempt to demonstrate an evolutionary relationship between humans and chimpanzees.1 The article showed that scientists incorporate a large amount of bias in their analyses in order to manipulate the data to support evolution, when in fact the DNA data support the obvious and distinctive categorization of life that is commonly observed in the fossil record and in existing life forms.
In reality, there is a clear demarcation between each created kind (humans, chimps, mice, chickens, dogs, etc.), and there is no blending together or observed transition from one kind of animal to another. All created kinds exhibit a certain amount of genetic variability within their grouping while still maintaining specific genetic boundaries. In other words, one kind does not change into another, either in the fossil record or in observations of living organisms.
Similar DNA Sequences
While the genome of each created kind is unique, many animal kinds share some specific types of genes that are generally similar in DNA sequence. When comparing DNA sequences between animal taxa, evolutionary scientists often hand-select the genes that are commonly shared and more similar (conserved), while giving less attention to categories of DNA sequence that are dissimilar. One result of this approach is that comparing the more conserved sequences allows the scientists to include more animal taxa in their analysis, giving a broader data set so they can propose a larger evolutionary tree.
Although these types of genes can be easily aligned and compared, the overall approach is biased towards evolution. It also avoids the majority of genes and sequences that would give a better understanding of DNA similarity concepts.
Tumor Suppressor Genes
As an example, there is a group of genes that not only have been used in evolutionary studies, but also have a significant impact on human health: the tumor suppressor genes. Aberrations within tumor suppressor genes can lead to cancer, thus it is important that their sequences remain unaltered. These genes tend to be very similar across many types of animals, making them ideal for comparative purposes. The close similarities of these genes between many animal taxa have led to their use by scientists in an attempt to prove evolution or common descent.2 What is really going on with these types of similar genes and how can they be interpreted within a special creation model as opposed to a naturalistic framework?
In very general terms, tumor suppressor genes are key genomic features (blocks of genetic code) that help regulate the growth and division of animal cells. When these genes are functioning properly, they code for proteins that can prevent or inhibit the out-of-control cell proliferation that forms the basis for the growth of tumors. When tumor suppressor genes are inactivated due to a DNA mutation, cell growth and division are no longer kept in check, resulting in cancer.
There are three main types of tumor suppressor genes. One type signals cells to slow down and stop dividing. Another type of tumor suppressor gene produces a protein that is responsible for checking and fixing damage in DNA that can happen when cells divide and proliferate. A third is responsible for telling cells when to die in a process called apoptosis. Cell growth, proliferation, and controlled cell death are essential to the development and maintenance of all animal systems.
For example, human hands develop from an initial fan-shaped structure, where apoptosis (programmed cell death) removes cells between fingers, and cell growth and division build up the fingers. How these genes are regulated will vary with the organism. However, because the basic aspects of the cell cycle are generally similar in many animals, one would actually expect a high level of DNA sequence conservation (similarity) between the coding parts of the genes as well as the proteins they produce.
The Ultimate Genetic Programmer
Generally, the more common a cellular process is between organisms, the more similar its various components will be. Does this indicate random chance evolutionary processes, or could it be an example of the Creator’s wise and efficient use and re-use of genetic code in different creatures to accomplish a common and basic cellular function?
Consider the computer world. Ask seasoned computer programmers how often they completely re-write long, complicated blocks of code when they already have what they need somewhere on file. When a long piece of previously-written code is needed and available, programmers will tailor it to fit in its new context, but they will usually not completely re-write it.
Of course, God is the ultimate programmer, and the genetic code He developed will produce the best possible protein needed for the system in which it works. If another organism has a similar physiology, one can expect many of the same genes to be present in its genome. There are a finite number of ways to accomplish the same task in cells. Thus, the genes that are used to accomplish that task will usually be quite similar, with minor key variations. These slight differences exist because the Creator has optimized the genes for that particular kind of creature and its biochemistry.
What the data really show is that high levels of efficiency and utility in genetic information seem to be a recurring theme in the study of genomes. In fact, with the limited number of genes in the human genome (about 25,000), over one million different protein variants are derived.3 Although not the topic of this article, a single animal gene can code for a wide variety of different proteins through a variety of complicated regulatory mechanisms. When scientists discovered this phenomenon, it totally negated the one-gene/one-protein mentality that originally existed when DNA sequence first began to be studied. That is pretty efficient code usage, which has never been equaled by even the most complex computer programs devised by man.
Genetic Regulatory Elements
While evolutionists have focused on genes that code for proteins, work is just beginning on an equally essential and complicated class of DNA sequence called regulatory elements. These are DNA sequences that do not code for protein but are involved in the regulation of genes. While efficient code usage and re-usage is common among many genomes, what is important is not just the protein the gene generates, but how much, how often, how fast, and when and where in the body it is produced. This is where the gene regulatory process begins to get really complicated. These regulatory differences play a key role in defining what makes a certain kind of organism unique.
After the human genome sequence was obtained to a completion level satisfactory to the scientific community, a separate but heavily-funded and related effort was initiated called the ENCODE (ENCyclopedia of DNA Elements) project.4 This involves ongoing research to determine the identity and characteristics of the regulatory elements in the human genome. At present, ENCODE has barely scratched the surface, but the results have revolutionized the concept of genetics by showing whole new levels of complexity and efficiency of code and gene activation.
The genetic picture that is beginning to emerge is one of incredible networked and regulatory complexity combined with an extremely high level of efficiency in code usage--certainly nothing that could have evolved on its own through chance random evolutionary processes. As is easily seen, trying to use common genes related to common processes as proof of evolution quickly falls apart in light of the bigger genomic picture. In fact, it really speaks of smart coding by the ultimate bio-systems programmer--God Himself.
The are fundamental differences between archaeal and bacterial–eukaryotic phospholipids and, more specifically, the apparently unrelated nature of the pathways that synthesize the two opposed glycerol phosphate stereoisomers 13 The asymmetry of the glycerol phosphate stereoisomers — G1P in archaea and G3P in bacteria and eukaryotes —that are synthesized by non-homologous glycerol phosphate dehydrogenases is the only inviolate difference.
If its inviolable, it means the membranes had to emerge separately.
10) W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science 284 (1999): 2124–28. W. Ford Doolittle, “Lateral Genomics,” Trends in Biochemical Sciences 24 (1999): M5– M8. W. Ford Doolittle, “Uprooting the Tree of Life,” Scientific American 282 (February, 2000): 90– 95.
11) Carl Woese, “On the evolution of cells,” Proceedings of the National Academy of Sciences USA 99 (2002): 8742–47. Carl R. Woese, “A New Biology for a New Century,” Microbiology and Molecular Biology Reviews 68 (2004): 173–86. Eric Bapteste, Yan Boucher, Jessica Leigh, and W. Ford Doolittle, “Phylogenetic Reconstruction and Lateral Gene Transfer,” Trends in Microbiology 12 (2004), 406–11. E. Bapteste, E. Susko, J. Leigh, D. MacLeod, R. L. Charlebois, and W. F. Doolittle, “Do Orthologous Gene Phylogenies Really Support Tree-Thinking?” Biomed Central Evolutionary Biology 5 (2005), 33. Available online (June 2006) at: http://www.biomedcentral.com/content/pdf/1471-2148-5-33.pdf. S. L. Baldauf, “The Deep Roots of Eukaryotes,” Science 300 (2003), 1703–06.
16. Intracellular Calcium, page 577
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